Install the shareware version on some windows pc and copy the DUKE3D.GRP to your linux box somehow.
You can also use the duke3d.cfg that you get, just be sure to change the screen res to 1024x768 (better just to use that gentoo file...)
I tested it the DUKE3D.GRP from the full 1.3 version --it works.
But with the Atomic Edition you get that extra forth set of levels.
So if you have a copy of Duke Nukem Atomic Edition laying around you're better off using that.

DEFS.CON, GAME.CON, USER.CON
read the docs that come with the source from CVS.
These files are in there somewhere (after compiling it), and you need to put them in the same directory with DUKE3D.GRP and duke3d and they need to have uppercase names.
I put everything in /usr/local/games/duke3d

That's pretty much it.
I made a launcher script too.
Put it on a button in the launcher gizmo in xfce4:

#!bin/sh

cd /usr/local/games/duke3d #put all those files in here

./duke3d

I even found a duke icon somewhere and put it on the launcher.

Oh yea... for those of you still stuck on windows (everybody else I guess) you can do this one instead: